RetrogeneDB ID:

retro_hsap_1563

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:15:44281261..44282382(-)
Located in intron of:ENSG00000171877
Retrocopy
information
Ensembl ID:ENSG00000185607
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ACTB
Ensembl ID:ENSG00000075624
Aliases:ACTB, BRWS1, PS1TP5BP1
Description:actin, beta [Source:HGNC Symbol;Acc:132]


Retrocopy-Parental alignment summary:






>retro_hsap_1563
ATGGATGATGATATCACCATGCTTGTCGTCGACAATGGCTCTGGCATGTGCAAGGCCAGCTTTGCAGGTGACGATGCCCA
CCCCGGGCCATCTTCCCCTTCATTGTGGGGCGCCCCAGACACCAGGGCGTGACGGTGGGCATGGGTCAGAAGGACTCCTA
TGTGGGCAACGAGGTCCAGAGCAAGAGAGGCATCCTGACCCTGAAGTACCCCATCAAGCAGGACATTGTCACCACCTGGG
ACGACATGGAGAAGATCTGGCACCACACCTTCTACAACGAGCTGTGTGTGGCTGCCAAGGAGCACCCCATGCTGCTGACC
AAGGTCCCCCTGAGCCCCAAGGCCAACCACAAGAAGATGACCCAGATCATGTTGGAGATCTTCGACAGGCCAGCCATGTA
CGTGGCCATCCAGGCCGTGCTGTCCCTGTACACCTCTGGCCTACCACTGACATCGTGATGGACTACGATGACGGGGTCAC
CCACACTGTGCCCATCTATGAAGAGTATGCCCTCCCCCATGCCATCCTGCGTGTGTGCCTGGCTGGTCAGGACCTGACTG
ACTACCTCATGAAGGTCCTCACCTAGCACAGCTACATCTTCACCGCCACAGCCAAGCGGGAAATTGTGCATGACATCAAG
GAGAAGCTGTGCTATGTCACCCTGGACTTCGAGCAGGAGATGGCCATGGTGGCCTCCAGCTCCTCCCTGGAGATAGCTAC
AAGCTGCCCGACGGCCAGGTCATCATCATCGGCAAAAGCAGTTCTGCTGCCCTGAGGCGCTCTTCCAGCCTTCCTTCCTG
GGCATGGAATCCCGCGGCATCCATGAAACTACCTTCAACTCCATCATGAAGTGTGATGTGGACATCCTCAAAGACCCGTA
TGCCAACACAGTGCTATCTGGCGGCACCACCAGGTACCCTGGCATCGCCGATAGGATGCAGAAGATCACCACCCTGGCGC
CCAGCACAATGAAGATCAAGATCACTGCTCCTCCCAAGCGCAAGTACTCCGTGTGGATCGGCAGCTCCATCCTGGCCTGG
CTGTCCACCGTCCAGCAGATGTGGATCAGCAAGCAGGAATATGATGAGTCAGGCACCTCCATCATCCACCGCAGATGCTT
C

ORF - retro_hsap_1563 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.79 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMDDDIAALVVDNGSGMCKAGFAGDDA-PRAVFPS-IVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLK
MDDDI..LVVDNGSGMCKA.FAGDDA.P....PS.IVGRPRHQGV.VGMGQKDSYVG.E.QSKRGILTLK
RetrocopyMDDDITMLVVDNGSGMCKASFAGDDAHPGPSSPS<IVGRPRHQGVTVGMGQKDSYVGNEVQSKRGILTLK
ParentalYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQA
YPI...IVT.WDDMEKIWHHTFYNEL.VA..EHP.LLT..PL.PKAN..KMTQIM.E.F..PAMYVAIQA
RetrocopyYPIKQDIVTTWDDMEKIWHHTFYNELCVAAKEHPMLLTKVPLSPKANHKKMTQIMLEIFDRPAMYVAIQA
ParentalVLSLYASG-RTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAERE
VLSLY.SG..TT.IVMD..DGVTHTVPIYE.YALPHAILR..LAG.DLTDYLMK.LT...Y.FT.TA.RE
RetrocopyVLSLYTSG<PTTDIVMDYDDGVTHTVPIYEEYALPHAILRVCLAGQDLTDYLMKVLT*HSYIFTATAKRE
ParentalIVRDIKEKLCYVALDFEQEMATAASSSSLE-KSYELPDGQVITIG-NERFRCPEALFQPSFLGMESCGIH
IV.DIKEKLCYV.LDFEQEMA..ASSSSLE..SY.LPDGQVI.IG....F.CPEALFQPSFLGMES.GIH
RetrocopyIVHDIKEKLCYVTLDFEQEMAMVASSSSLE<DSYKLPDGQVIIIG<QKQFCCPEALFQPSFLGMESRGIH
ParentalETTFNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSI
ETTFNSIMKCDVDI.KD.YANTVLSGGTT.YPGIADRMQK.IT.LAPSTMKIKI.APP.RKYSVWIG.SI
RetrocopyETTFNSIMKCDVDILKDPYANTVLSGGTTRYPGIADRMQK-ITTLAPSTMKIKITAPPKRKYSVWIGSSI
ParentalLASLSTFQQMWISKQEYDESGPSIVHRKCF
LA.LST.QQMWISKQEYDESG.SI.HR.CF
RetrocopyLAWLSTVQQMWISKQEYDESGTSIIHRRCF

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
bodymap2_adipose 0 .02 RPM 5336 .71 RPM
bodymap2_adrenal 0 .02 RPM 5105 .37 RPM
bodymap2_brain 0 .16 RPM 2354 .74 RPM
bodymap2_breast 0 .02 RPM 3342 .68 RPM
bodymap2_colon 0 .02 RPM 6846 .79 RPM
bodymap2_heart 0 .02 RPM 595 .89 RPM
bodymap2_kidney 0 .10 RPM 2141 .79 RPM
bodymap2_liver 0 .00 RPM 1498 .34 RPM
bodymap2_lung 0 .00 RPM 6019 .68 RPM
bodymap2_lymph_node 0 .02 RPM 3028 .73 RPM
bodymap2_ovary 0 .12 RPM 4495 .81 RPM
bodymap2_prostate 0 .07 RPM 6984 .69 RPM
bodymap2_skeletal_muscle 0 .00 RPM 729 .01 RPM
bodymap2_testis 0 .19 RPM 2997 .25 RPM
bodymap2_thyroid 0 .23 RPM 1886 .18 RPM
bodymap2_white_blood_cells 0 .00 RPM 9289 .16 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1563 was not detected

EST - click to see more details

1 EST(s) were mapped to retro_hsap_1563 retrocopy
EST ID Start End Identity Match Mis-match Score
CN273804 44281349 44281824 100 475 0 475

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_43836599 libraries690 libraries504 libraries36 libraries0 libraries
TSS #2 TSS_43837807 libraries686 libraries323 libraries10 libraries3 libraries

The graphical summary, for retro_hsap_1563 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_1563 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1563 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1051
Gorilla gorilla retro_ggor_1188
Pongo abelii retro_pabe_1292
Parental genes homology:
Parental genes homology involve 22 parental genes, and 99 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000066011 retrocopy
retro_amel_11,
Cavia porcellus ENSCPOG000000134671 retrocopy
retro_cpor_60,
Homo sapiens ENSG00000075624 6 retrocopies
retro_hsap_1563 , retro_hsap_1894, retro_hsap_3386, retro_hsap_38, retro_hsap_4204, retro_hsap_518,
Homo sapiens ENSG000001381071 retrocopy
retro_hsap_2141,
Homo sapiens ENSG0000018400910 retrocopies
retro_hsap_1548, retro_hsap_1607, retro_hsap_2405, retro_hsap_2591, retro_hsap_2605, retro_hsap_3466, retro_hsap_3631, retro_hsap_409, retro_hsap_4818, retro_hsap_4935,
Gallus gallus ENSGALG000000096211 retrocopy
retro_ggal_4,
Gorilla gorilla ENSGGOG0000000113318 retrocopies
retro_ggor_1177, retro_ggor_1188, retro_ggor_1211, retro_ggor_1266, retro_ggor_1297, retro_ggor_1332, retro_ggor_1387, retro_ggor_1622, retro_ggor_1825, retro_ggor_1890, retro_ggor_2292, retro_ggor_2774, retro_ggor_2817, retro_ggor_3002, retro_ggor_352, retro_ggor_405, retro_ggor_44, retro_ggor_477,
Loxodonta africana ENSLAFG000000091671 retrocopy
retro_lafr_116,
Meleagris gallopavo ENSMGAG000000039602 retrocopies
retro_mgal_5, retro_mgal_6,
Macaca mulatta ENSMMUG000000111531 retrocopy
retro_mmul_135,
Mustela putorius furoENSMPUG000000166122 retrocopies
retro_mputfur_440, retro_mputfur_461,
Mus musculus ENSMUSG000000295807 retrocopies
retro_mmus_1613, retro_mmus_1677, retro_mmus_283, retro_mmus_2880, retro_mmus_3411, retro_mmus_3532, retro_mmus_761,
Ornithorhynchus anatinus ENSOANG000000077162 retrocopies
retro_oana_4, retro_oana_8,
Otolemur garnettii ENSOGAG000000083481 retrocopy
retro_ogar_2637,
Petromyzon marinus ENSPMAG000000041611 retrocopy
retro_pmar_4,
Pongo abelii ENSPPYG0000001733623 retrocopies
retro_pabe_1281, retro_pabe_1292, retro_pabe_1575, retro_pabe_1610, retro_pabe_1772, retro_pabe_1816, retro_pabe_1911, retro_pabe_2042, retro_pabe_2168, retro_pabe_2175, retro_pabe_2188, retro_pabe_227, retro_pabe_2754, retro_pabe_2811, retro_pabe_2824, retro_pabe_2862, retro_pabe_2978, retro_pabe_309, retro_pabe_3563, retro_pabe_3567, retro_pabe_3746, retro_pabe_745, retro_pabe_86,
Rattus norvegicus ENSRNOG0000003425410 retrocopies
retro_rnor_1324, retro_rnor_1386, retro_rnor_1799, retro_rnor_2371, retro_rnor_2714, retro_rnor_2856, retro_rnor_2978, retro_rnor_351, retro_rnor_459, retro_rnor_935,
Sarcophilus harrisii ENSSHAG000000126944 retrocopies
retro_shar_120, retro_shar_370, retro_shar_62, retro_shar_93,
Sus scrofa ENSSSCG000000075851 retrocopy
retro_sscr_548,
Ictidomys tridecemlineatus ENSSTOG000000068682 retrocopies
retro_itri_1675, retro_itri_531,
Ictidomys tridecemlineatus ENSSTOG000000147973 retrocopies
retro_itri_149, retro_itri_1881, retro_itri_4,
Xenopus tropicalis ENSXETG000000251161 retrocopy
retro_xtro_6,

Expression level across human populations :
image/svg+xml GBR_HG00142 GBR_HG00099 GBR_HG00114 GBR_HG00143 GBR_HG00131 GBR_HG00137 GBR_HG00133 GBR_HG00119 GBR_HG00111 GBR_HG00134 FIN_HG00378 FIN_HG00338 FIN_HG00349 FIN_HG00375 FIN_HG00315 FIN_HG00277 FIN_HG00328 FIN_HG00321 FIN_HG00377 FIN_HG00183 TSI_NA20756 TSI_NA20538 TSI_NA20798 TSI_NA20532 TSI_NA20765 TSI_NA20518 TSI_NA20513 TSI_NA20512 TSI_NA20771 TSI_NA20786 YRI_NA19114 YRI_NA19099 YRI_NA18870 YRI_NA18907 YRI_NA19223 YRI_NA19214 YRI_NA18916 YRI_NA19093 YRI_NA19118 YRI_NA19213 Toscaniin Italia: Finnish inFinland: British in England and Scotland: Utah Residents (CEPH) with Northernand Western European Ancestry: Yoruba in Ibadan, Nigeria: CEU_NA12760 CEU_NA12827 CEU_NA12872 CEU_NA12751 CEU_NA12873 CEU_NA12400 CEU_NA11930 CEU_NA12004 CEU_NA11831 CEU_NA11843 No expression ( = 0 RPM ) > 0 RPM = 0.14 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .09 RPM
CEU_NA11843 0 .11 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .11 RPM
CEU_NA12751 0 .12 RPM
CEU_NA12760 0 .13 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .11 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .06 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .04 RPM
FIN_HG00349 0 .06 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .08 RPM
GBR_HG00099 0 .06 RPM
GBR_HG00111 0 .04 RPM
GBR_HG00114 0 .05 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .07 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .08 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .14 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .12 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .11 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .05 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .06 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .02 RPM
YRI_NA19223 0 .04 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).



Copyright © RetrogeneDB 2014-2017